A method and apparatus for performing cell cytometry mitigate or eliminate the effects of refraction that result from interfaces between materials having different refractive indices. Solid materials, such as the walls of a flow path, which materials are disposed between a nominal focal point and an objective lens, are formed of a material having a refractive index between 1.30 and 1.40 inclusive. The refractive index of a liquid material, such as an immersion fluid or a fluid carrying, suspending, or bathing an analyte, may be adjusted to have a refractive index closer to that of surrounding solid materials and, in particular, within 0.02 of the refractive index of the surrounding solid materials.